Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
20:09:07.877 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu May 28 20:09:07 GMT 2026] MarkDuplicates --INPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam --METRICS_FILE 22Rv1_FFPE_RNA_0001_B23LG7FLT4_2.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu May 28 20:09:07 GMT 2026] Executing as ?@nf-8d8a40ef9696c5adeaa6f9b31c6045f7-b6c2b-xbwsz on Linux 6.12.83 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-05-28 20:09:07 MarkDuplicates Start of doWork freeMemory: 105828016; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 20:09:07 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 20:09:07 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-28 20:09:12 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:45,341,086
INFO 2026-05-28 20:09:12 MarkDuplicates Tracking 2150 as yet unmatched pairs. 3 records in RAM.
INFO 2026-05-28 20:09:15 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:165,654,295
INFO 2026-05-28 20:09:15 MarkDuplicates Tracking 4023 as yet unmatched pairs. 1 records in RAM.
INFO 2026-05-28 20:09:18 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-05-28 20:09:18 MarkDuplicates Tracking 53413 as yet unmatched pairs. 3075 records in RAM.
INFO 2026-05-28 20:09:20 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr2:189,006,343
INFO 2026-05-28 20:09:20 MarkDuplicates Tracking 55801 as yet unmatched pairs. 1120 records in RAM.
INFO 2026-05-28 20:09:23 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 3s. Last read position: chr3:50,297,159
INFO 2026-05-28 20:09:23 MarkDuplicates Tracking 53852 as yet unmatched pairs. 1391 records in RAM.
INFO 2026-05-28 20:09:26 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr4:22,442,754
INFO 2026-05-28 20:09:26 MarkDuplicates Tracking 52146 as yet unmatched pairs. 1055 records in RAM.
INFO 2026-05-28 20:09:29 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr5:118,973,773
INFO 2026-05-28 20:09:29 MarkDuplicates Tracking 50260 as yet unmatched pairs. 1654 records in RAM.
INFO 2026-05-28 20:09:31 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 2s. Last read position: chr6:26,156,731
INFO 2026-05-28 20:09:31 MarkDuplicates Tracking 48353 as yet unmatched pairs. 2900 records in RAM.
INFO 2026-05-28 20:09:33 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr6:111,274,281
INFO 2026-05-28 20:09:33 MarkDuplicates Tracking 46241 as yet unmatched pairs. 770 records in RAM.
INFO 2026-05-28 20:09:37 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr7:75,421,834
INFO 2026-05-28 20:09:37 MarkDuplicates Tracking 44435 as yet unmatched pairs. 1627 records in RAM.
INFO 2026-05-28 20:09:40 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 3s. Last read position: chr8:30,504,372
INFO 2026-05-28 20:09:40 MarkDuplicates Tracking 42487 as yet unmatched pairs. 1949 records in RAM.
INFO 2026-05-28 20:09:42 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 1s. Last read position: chr8:144,180,441
INFO 2026-05-28 20:09:42 MarkDuplicates Tracking 40709 as yet unmatched pairs. 143 records in RAM.
INFO 2026-05-28 20:09:44 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr9:134,765,706
INFO 2026-05-28 20:09:44 MarkDuplicates Tracking 38839 as yet unmatched pairs. 373 records in RAM.
INFO 2026-05-28 20:09:47 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr10:119,042,185
INFO 2026-05-28 20:09:47 MarkDuplicates Tracking 36940 as yet unmatched pairs. 196 records in RAM.
INFO 2026-05-28 20:09:49 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr11:65,554,300
INFO 2026-05-28 20:09:49 MarkDuplicates Tracking 34908 as yet unmatched pairs. 1613 records in RAM.
INFO 2026-05-28 20:09:51 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr12:11,853,467
INFO 2026-05-28 20:09:51 MarkDuplicates Tracking 32866 as yet unmatched pairs. 2591 records in RAM.
INFO 2026-05-28 20:09:54 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr12:119,179,587
INFO 2026-05-28 20:09:54 MarkDuplicates Tracking 30894 as yet unmatched pairs. 610 records in RAM.
INFO 2026-05-28 20:09:58 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr14:51,720,247
INFO 2026-05-28 20:09:58 MarkDuplicates Tracking 28983 as yet unmatched pairs. 1767 records in RAM.
INFO 2026-05-28 20:10:01 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 3s. Last read position: chr14:105,708,566
INFO 2026-05-28 20:10:01 MarkDuplicates Tracking 27316 as yet unmatched pairs. 82 records in RAM.
INFO 2026-05-28 20:10:04 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 3s. Last read position: chr16:2,037,885
INFO 2026-05-28 20:10:04 MarkDuplicates Tracking 25381 as yet unmatched pairs. 2651 records in RAM.
INFO 2026-05-28 20:10:06 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr16:30,700,847
INFO 2026-05-28 20:10:06 MarkDuplicates Tracking 23986 as yet unmatched pairs. 1248 records in RAM.
INFO 2026-05-28 20:10:10 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 3s. Last read position: chr17:9,916,995
INFO 2026-05-28 20:10:10 MarkDuplicates Tracking 21808 as yet unmatched pairs. 3812 records in RAM.
INFO 2026-05-28 20:10:12 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,354
INFO 2026-05-28 20:10:12 MarkDuplicates Tracking 19984 as yet unmatched pairs. 1978 records in RAM.
INFO 2026-05-28 20:10:16 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:06s. Time for last 1,000,000: 3s. Last read position: chr18:49,814,363
INFO 2026-05-28 20:10:16 MarkDuplicates Tracking 17651 as yet unmatched pairs. 261 records in RAM.
INFO 2026-05-28 20:10:18 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr19:15,257,094
INFO 2026-05-28 20:10:18 MarkDuplicates Tracking 15342 as yet unmatched pairs. 3855 records in RAM.
INFO 2026-05-28 20:10:21 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr19:45,306,833
INFO 2026-05-28 20:10:21 MarkDuplicates Tracking 12899 as yet unmatched pairs. 1397 records in RAM.
INFO 2026-05-28 20:10:24 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 3s. Last read position: chr20:50,191,214
INFO 2026-05-28 20:10:24 MarkDuplicates Tracking 10646 as yet unmatched pairs. 551 records in RAM.
INFO 2026-05-28 20:10:27 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr21:8,217,285
INFO 2026-05-28 20:10:27 MarkDuplicates Tracking 9044 as yet unmatched pairs. 3114 records in RAM.
INFO 2026-05-28 20:10:29 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr21:8,399,111
INFO 2026-05-28 20:10:29 MarkDuplicates Tracking 8233 as yet unmatched pairs. 2293 records in RAM.
INFO 2026-05-28 20:10:31 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr21:8,444,115
INFO 2026-05-28 20:10:31 MarkDuplicates Tracking 6903 as yet unmatched pairs. 961 records in RAM.
INFO 2026-05-28 20:10:33 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:23s. Time for last 1,000,000: 2s. Last read position: chr22:31,260,007
INFO 2026-05-28 20:10:33 MarkDuplicates Tracking 5189 as yet unmatched pairs. 1148 records in RAM.
INFO 2026-05-28 20:10:36 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chrX:143,581,717
INFO 2026-05-28 20:10:36 MarkDuplicates Tracking 3175 as yet unmatched pairs. 257 records in RAM.
INFO 2026-05-28 20:10:39 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: GL000220.1:116,792
INFO 2026-05-28 20:10:39 MarkDuplicates Tracking 2521 as yet unmatched pairs. 43 records in RAM.
INFO 2026-05-28 20:10:41 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 2s. Last read position: KI270733.1:128,201
INFO 2026-05-28 20:10:41 MarkDuplicates Tracking 2458 as yet unmatched pairs. 2455 records in RAM.
INFO 2026-05-28 20:10:43 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: KI270733.1:176,024
INFO 2026-05-28 20:10:43 MarkDuplicates Tracking 77 as yet unmatched pairs. 74 records in RAM.
INFO 2026-05-28 20:10:44 MarkDuplicates Read 35698267 records. 0 pairs never matched.
INFO 2026-05-28 20:10:46 MarkDuplicates After buildSortedReadEndLists freeMemory: 15225106104; totalMemory: 21709717504; maxMemory: 63585648640
INFO 2026-05-28 20:10:46 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 20:10:53 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 20:10:58 OpticalDuplicateFinder Large duplicate set. size = 1037
INFO 2026-05-28 20:10:58 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:2,982
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder Large duplicate set. size = 1516
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:28,231
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder Large duplicate set. size = 1357
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,988
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder Large duplicate set. size = 1060
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-15,705
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder Large duplicate set. size = 1191
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:12,407
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder Large duplicate set. size = 1472
INFO 2026-05-28 20:10:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:24,243
INFO 2026-05-28 20:11:00 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 20:11:04 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 20:11:05 MarkDuplicates After generateDuplicateIndexes freeMemory: 23476436576; totalMemory: 39426457600; maxMemory: 63585648640
INFO 2026-05-28 20:11:05 MarkDuplicates Marking 18051978 records as duplicates.
INFO 2026-05-28 20:11:05 MarkDuplicates Found 305008 optical duplicate clusters.
INFO 2026-05-28 20:11:05 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 20:11:34 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:29s. Time for last 10,000,000: 29s. Last read position: chr7:75,421,834
INFO 2026-05-28 20:12:00 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:54s. Time for last 10,000,000: 25s. Last read position: chr16:2,037,885
INFO 2026-05-28 20:12:25 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:20s. Time for last 10,000,000: 25s. Last read position: chr21:8,444,115
INFO 2026-05-28 20:12:41 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 20:12:41 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 20:12:41 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 20:12:42 MarkDuplicates Before output close freeMemory: 202089336; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-05-28 20:12:42 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 20:12:42 MarkDuplicates After output close freeMemory: 104297200; totalMemory: 134217728; maxMemory: 63585648640
[Thu May 28 20:12:42 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 3.57 minutes.
Runtime.totalMemory()=134217728
ls: *cram: No such file or directory
ls: *.crai: No such file or directory